Manganese in PDB 2je9: Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose

The structure of Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose, PDB code: 2je9 was solved by C.S.Nagano, L.Sanz, B.S.Cavada, J.J.Calvete, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.71 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.171, 85.153, 175.741, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.9

The structure of Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose also contains other interesting chemical elements:

Bromine	(Br)	4 atoms
Chlorine	(Cl)	4 atoms
Calcium	(Ca)	4 atoms

The binding sites of Manganese atom in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose (pdb code 2je9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose, PDB code: 2je9:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1241 b:13.4 occ:1.00 OD1 A:ASP21 2.2 17.6 1.0 O A:HOH2139 2.2 17.1 1.0 O A:HOH2138 2.2 12.9 1.0 OD1 A:ASP12 2.2 11.6 1.0 OE2 A:GLU10 2.2 13.6 1.0 NE2 A:HIS26 2.3 7.5 1.0 CG A:ASP21 3.2 15.8 1.0 CG A:ASP12 3.2 11.5 1.0 CE1 A:HIS26 3.2 5.6 1.0 CD A:GLU10 3.3 17.2 1.0 CD2 A:HIS26 3.3 6.5 1.0 CB A:ASP12 3.6 11.1 1.0 OE1 A:GLU10 3.6 18.6 1.0 OD2 A:ASP21 3.6 13.8 1.0 O A:HOH2131 4.0 9.1 1.0 O A:HOH2011 4.1 24.8 1.0 OG A:SER36 4.2 12.7 1.0 CA A:CA1240 4.2 12.1 1.0 O A:HOH2012 4.2 19.6 1.0 OD2 A:ASP12 4.3 14.3 1.0 ND1 A:HIS26 4.4 4.6 1.0 CB A:ASP21 4.4 15.9 1.0 CG A:HIS26 4.4 9.3 1.0 O A:ILE34 4.6 15.3 1.0 CG A:GLU10 4.6 12.8 1.0 CA A:ASP21 4.7 17.1 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1241 b:16.9 occ:1.00 O B:HOH2131 1.8 16.5 1.0 OD1 B:ASP12 2.0 19.2 1.0 O B:HOH2130 2.2 18.6 1.0 NE2 B:HIS26 2.2 14.0 1.0 OD1 B:ASP21 2.3 25.0 1.0 OE2 B:GLU10 2.3 19.1 1.0 CG B:ASP12 3.0 17.4 1.0 CE1 B:HIS26 3.1 13.8 1.0 CG B:ASP21 3.2 23.2 1.0 CD2 B:HIS26 3.2 12.8 1.0 CD B:GLU10 3.3 19.2 1.0 CB B:ASP12 3.5 15.8 1.0 OE1 B:GLU10 3.6 20.1 1.0 OD2 B:ASP21 3.6 18.5 1.0 OD2 B:ASP12 4.1 16.9 1.0 O B:HOH2122 4.1 15.3 1.0 O B:HOH2008 4.1 29.7 1.0 OG B:SER36 4.2 18.2 1.0 ND1 B:HIS26 4.3 13.1 1.0 CA B:CA1240 4.3 18.4 1.0 CB B:ASP21 4.3 23.9 1.0 CG B:HIS26 4.3 16.5 1.0 CA B:ASP21 4.6 24.8 1.0 CG B:GLU10 4.6 17.4 1.0 O B:ILE34 4.7 24.3 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1241 b:21.2 occ:1.00 O C:HOH2078 1.8 9.2 1.0 O C:HOH2079 2.1 22.5 1.0 OD1 C:ASP12 2.2 15.2 1.0 OE2 C:GLU10 2.2 20.8 1.0 OD1 C:ASP21 2.3 25.0 1.0 NE2 C:HIS26 2.3 21.9 1.0 CE1 C:HIS26 3.1 17.6 1.0 CG C:ASP21 3.1 26.3 1.0 CD C:GLU10 3.2 24.0 1.0 CG C:ASP12 3.2 21.8 1.0 CD2 C:HIS26 3.4 19.3 1.0 OE1 C:GLU10 3.4 24.8 1.0 OD2 C:ASP21 3.4 21.3 1.0 CB C:ASP12 3.6 20.9 1.0 O C:HOH2074 3.8 27.7 1.0 CA C:CA1240 4.1 26.3 1.0 ND1 C:HIS26 4.2 19.3 1.0 CB C:ASP21 4.3 27.9 1.0 OD2 C:ASP12 4.3 25.5 1.0 OG C:SER36 4.4 22.4 1.0 CG C:HIS26 4.4 19.8 1.0 O C:ILE34 4.6 25.4 1.0 CG C:GLU10 4.6 20.1 1.0 CA C:ASP21 4.7 28.7 1.0 O C:HOH2007 4.9 30.4 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1241 b:16.9 occ:1.00 O D:HOH2083 1.9 11.3 1.0 OD1 D:ASP12 2.0 16.7 1.0 NE2 D:HIS26 2.2 14.7 1.0 O D:HOH2082 2.2 14.2 1.0 OD1 D:ASP21 2.2 14.8 1.0 OE2 D:GLU10 2.3 18.6 1.0 CE1 D:HIS26 3.0 12.3 1.0 CG D:ASP12 3.1 19.4 1.0 CG D:ASP21 3.1 18.7 1.0 CD2 D:HIS26 3.2 13.5 1.0 CD D:GLU10 3.2 19.1 1.0 OD2 D:ASP21 3.5 16.3 1.0 CB D:ASP12 3.5 17.9 1.0 OE1 D:GLU10 3.5 20.3 1.0 O D:HOH2077 4.0 23.7 1.0 OD2 D:ASP12 4.2 19.7 1.0 ND1 D:HIS26 4.2 12.6 1.0 OG D:SER36 4.2 17.5 1.0 CA D:CA1240 4.2 19.7 1.0 CG D:HIS26 4.3 13.7 1.0 CB D:ASP21 4.3 18.5 1.0 CG D:GLU10 4.6 18.4 1.0 O D:ILE34 4.6 20.5 1.0 CA D:ASP21 4.7 18.5 1.0

C.S.Nagano, J.J.Calvete, D.Barettino, A.Perez, B.S.Cavada, L.Sanz. Insights Into the Structural Basis of the pH- Dependent Dimer-Tetramer Equilibrium Through Crystallographic Analysis of Recombinant Diocleinae Lectins. Biochem.J. V. 409 417 2008.
ISSN: ISSN 0264-6021
PubMed: 17937659
DOI: 10.1042/BJ20070942